added missing import statement for gzip
added functions for downsampling and matching sample sizes
Moved parse_genes.py script over from scripts repo
get stats for every chromosome
added function to create Coord objects from list or array of sites
Allow input to be read from stdin. Allow scores to be floats.
Warn when rounding floats to ints though.
Added utility program to split BED files into separate BED files
for each chromosome
handle gl chromosomes that are present in hg19
corrected comment
improved speed of listing tracks
-- only check if dir if file does not end with .h5
added util.check_open convenience function
-- handles both .gz and regular files
-- does not allow existing files to be overwritten
   (checks for existance before write-open)
added kmer cython module for counting kmers etc.
improved usage message
handle different ways of naming fly chromosomes
ignore cython-generated kmer.c file
default to what is specified in GENOME_ASSEMBLY env var, not hg18
allow lowercase nucleotide chars to be converted to IDs
removed compilation of test.c, which no longer exists
added ability to read int16 datatype from tab-delimited txt files
Wrote a program to calculate mappability of every base
Takes into account SNPs